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annotate crop_image.xml @ 0:f8bfa85cac4c draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
author imgteam
date Fri, 06 Jun 2025 12:46:50 +0000
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f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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diff changeset
1 <tool id="ip_crop_image" name="Crop image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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2 <description>with giatools</description>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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3 <macros>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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4 <import>creators.xml</import>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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5 <import>tests.xml</import>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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6 <token name="@TOOL_VERSION@">0.4.1</token>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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7 <token name="@VERSION_SUFFIX@">0</token>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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8 </macros>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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9 <creator>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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10 <expand macro="creators/bmcv" />
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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11 </creator>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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12 <edam_operations>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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13 <edam_operation>operation_3443</edam_operation>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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14 </edam_operations>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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15 <xrefs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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16 <xref type="bio.tools">giatools</xref>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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17 </xrefs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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18 <requirements>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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19 <requirement type="package" version="@TOOL_VERSION@">giatools</requirement>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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20 </requirements>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
imgteam
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21 <command detect_errors="aggressive"><![CDATA[
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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22
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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23 mkdir ./output &&
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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24 python '$__tool_directory__/crop_image.py'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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25
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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26 '$image'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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27 '$labelmap'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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28 '$skip_labels'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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29 '${image.ext}'
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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30
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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31 ./output
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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32
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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33 ]]></command>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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34 <inputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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35 <param name="image" type="data" format="png,tiff" label="Image file" help="The image to be cropped."/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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36 <param name="labelmap" type="data" format="png,tiff" label="Label map" help="Each label identifies an individual region of interest, for which a cropped image is produced."/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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37 <param name="skip_labels" type="text" label="Skip labels" value="0" optional="true" help="Comma-separated list of labels for which no cropped image shall be produced.">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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38 <validator type="regex">^\d+(,\d+)*$|^$</validator>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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39 </param>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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40 </inputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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41 <outputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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42 <collection type="list" name="output" label="Crop ${on_string}" format_source="image">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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43 <discover_datasets directory="output" pattern="__name_and_ext__"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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44 </collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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45 </outputs>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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46 <tests>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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47 <!-- Test 2D TIFF -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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48 <test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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49 <param name="image" value="yx_float32.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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50 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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51 <output_collection name="output" type="list" count="2">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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52 <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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53 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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54 </output_collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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55 </test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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56 <!-- Test with `skip_labels` -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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57 <test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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58 <param name="image" value="yx_float32.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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59 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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60 <param name="skip_labels" value="0,1"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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61 <output_collection name="output" type="list" count="1">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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62 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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63 </output_collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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64 </test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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65 <!-- Test with empty `skip_labels` -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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66 <test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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67 <param name="image" value="yx_float32.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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68 <param name="labelmap" value="yx_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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69 <param name="skip_labels" value=""/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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70 <output_collection name="output" type="list" count="3">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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71 <expand macro="tests/intensity_image_diff/element" name="0" value="yx_float32_uint8_0.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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72 <expand macro="tests/intensity_image_diff/element" name="1" value="yx_float32_uint8_1.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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73 <expand macro="tests/intensity_image_diff/element" name="2" value="yx_float32_uint8_2.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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74 </output_collection>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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75 </test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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76 <!-- Test 3D TIFF (multi-frame) -->
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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77 <test>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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78 <param name="image" value="zyx_uint16.tiff" ftype="tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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79 <param name="labelmap" value="yxz_uint8.tiff"/>
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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80 <output_collection name="output" type="list" count="1">
f8bfa85cac4c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/crop_image/ commit 7a5037206d267aa7d9b7e5e062327c3464942471
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81 <expand macro="tests/intensity_image_diff/element" name="1" value="zyx_uint16_uint8_1.tiff" ftype="tiff"/>
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82 </output_collection>
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83 </test>
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84 <!-- Test PNG -->
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85 <test>
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86 <param name="image" value="yxc_uint8.png" ftype="png"/>
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87 <param name="labelmap" value="yxc_uint8_mask.png"/>
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88 <output_collection name="output" type="list" count="1">
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89 <expand macro="tests/intensity_image_diff/element" name="2" value="yxc_uint8_uint8_2.png" ftype="png"/>
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90 </output_collection>
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91 </test>
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92 </tests>
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93 <help>
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94
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95 **Crops an image using one or more regions of interest.**
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96
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97 The image is cropped using a label map that identifies individual regions of interest. The image and the label map must be of equal size.
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98
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99 This operation preserves the file type of the image, the brightness, and the range of values.
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100
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101 </help>
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102 <citations>
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103 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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104 </citations>
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105 </tool>